File: Test2DVertexBasedCryptRepresentativeSimulation Type: cpu Showing nodes accounting for 80485ms, 88.16% of 91293ms total Dropped 1097 nodes (cum <= 456.46ms) flat flat% sum% cum cum% 0 0% 0% 91056ms 99.74% __libc_start_call_main 0 0% 0% 91056ms 99.74% __libc_start_main_impl 0 0% 0% 91056ms 99.74% _start 0 0% 0% 91038ms 99.72% CxxTest::ErrorFormatter::run (inline) 0 0% 0% 91038ms 99.72% CxxTest::TestRunner::runAllTests (inline) 0 0% 0% 91038ms 99.72% CxxTest::TestRunner::runWorld (inline) 0 0% 0% 91038ms 99.72% main 0 0% 0% 91005ms 99.68% CxxTest::TestRunner::runSuite (inline) 0 0% 0% 91005ms 99.68% CxxTest::TestRunner::runTest (inline) 0 0% 0% 91005ms 99.68% Test2DVertexCryptRepresentativeSimulation::Test2DVertexCryptRepresentativeSimulationForProfiling 5ms 0.0055% 0.0055% 90999ms 99.68% AbstractCellBasedSimulation::Solve 9ms 0.0099% 0.015% 48500ms 53.13% OffLatticeSimulation::UpdateCellLocationsAndTopology 15ms 0.016% 0.032% 45337ms 49.66% ForwardEulerNumericalMethod::UpdateAllNodePositions 41ms 0.045% 0.077% 44374ms 48.61% AbstractNumericalMethod::ComputeForcesIncludingDamping 276ms 0.3% 0.38% 34909ms 38.24% NagaiHondaForce::AddForceContribution 2ms 0.0022% 0.38% 31316ms 34.30% AbstractCellBasedSimulation::UpdateCellPopulation 1ms 0.0011% 0.38% 18504ms 20.27% VertexBasedCellPopulation::Update 1ms 0.0011% 0.38% 18402ms 20.16% MutableVertexMesh::ReMesh 8110ms 8.88% 9.27% 15807ms 17.31% Cylindrical2dVertexMesh::GetVectorFromAtoB 66ms 0.072% 9.34% 15279ms 16.74% Cell::ReadyToDivide 95ms 0.1% 9.44% 14476ms 15.86% NagaiHondaForce::GetAdhesionParameter 19ms 0.021% 9.46% 14440ms 15.82% AbstractPhaseBasedCellCycleModel::ReadyToDivide 63ms 0.069% 9.53% 12422ms 13.61% SimpleWntCellCycleModel::UpdateCellCyclePhase 356ms 0.39% 9.92% 12170ms 13.33% boost::numeric::ublas::c_vector::c_vector (partial-inline) 524ms 0.57% 10.50% 11553ms 12.65% std::__new_allocator::allocate (inline) 57ms 0.062% 10.56% 11327ms 12.41% CellPropertyCollection::GetPropertiesType (inline) 0 0% 10.56% 11042ms 12.10% std::allocator_traits::allocate (inline) 820ms 0.9% 11.46% 10946ms 11.99% operator new 202ms 0.22% 11.68% 10880ms 11.92% boost::numeric::ublas::vector_assign (inline) 0 0% 11.68% 10842ms 11.88% std::_Rb_tree::_M_create_node (inline) 0 0% 11.68% 10527ms 11.53% std::_Rb_tree::_M_get_node (inline) 3421ms 3.75% 15.43% 9830ms 10.77% __GI___libc_malloc 92ms 0.1% 15.53% 9492ms 10.40% AbstractCellProperty::IsSubType (inline) 2160ms 2.37% 17.89% 9400ms 10.30% __dynamic_cast 0 0% 17.89% 9361ms 10.25% std::_Rb_tree::_Alloc_node::operator() (inline) 99ms 0.11% 18.00% 9159ms 10.03% VertexBasedCellPopulation::GetDampingConstant 2ms 0.0022% 18.00% 9065ms 9.93% AbstractCellBasedSimulation::DoCellBirth 35ms 0.038% 18.04% 9041ms 9.90% AbstractTargetAreaModifier::UpdateTargetAreas 41ms 0.045% 18.09% 8968ms 9.82% SimpleTargetAreaModifier::UpdateTargetAreaOfCell 123ms 0.13% 18.22% 8428ms 9.23% MutableVertexMesh::CheckForIntersections 872ms 0.96% 19.18% 8275ms 9.06% std::_Rb_tree::_M_erase 0 0% 19.18% 8249ms 9.04% std::_Rb_tree::_M_drop_node (inline) 2365ms 2.59% 21.77% 7890ms 8.64% boost::numeric::ublas::indexing_vector_assign 304ms 0.33% 22.10% 7793ms 8.54% std::_Rb_tree::~_Rb_tree (inline) 91ms 0.1% 22.20% 7480ms 8.19% std::__new_allocator::deallocate (inline) 0 0% 22.20% 7467ms 8.18% std::allocator_traits::deallocate (inline) 0 0% 22.20% 7420ms 8.13% std::_Rb_tree::_M_put_node (inline) 45ms 0.049% 22.25% 7415ms 8.12% Cell::GetMutationState 0 0% 22.25% 7404ms 8.11% std::set::~set (inline) 1870ms 2.05% 24.30% 7259ms 7.95% __GI___libc_free 428ms 0.47% 24.77% 6996ms 7.66% VertexMesh::GetNextEdgeGradientOfElementAtNode 0 0% 24.77% 6867ms 7.52% std::set::insert (inline) 440ms 0.48% 25.25% 6841ms 7.49% std::map::operator[] (partial-inline) 36ms 0.039% 25.29% 6677ms 7.31% VertexBasedCellPopulation::GetLocationOfCellCentre 504ms 0.55% 25.84% 6410ms 7.02% VertexMesh::GetCentroidOfElement 10ms 0.011% 25.85% 6347ms 6.95% MutableVertexMesh::RemoveDeletedNodesAndElements 847ms 0.93% 26.78% 6332ms 6.94% std::_Rb_tree::_M_insert_ (inline) 420ms 0.46% 27.24% 6256ms 6.85% VertexMesh::ElementIncludesPoint 127ms 0.14% 27.38% 5929ms 6.49% std::_Rb_tree::_Rb_tree (partial-inline) 5884ms 6.45% 33.82% 5884ms 6.45% __strcmp_evex 46ms 0.05% 33.87% 5766ms 6.32% std::set_intersection (inline) 249ms 0.27% 34.15% 5720ms 6.27% std::__set_intersection 526ms 0.58% 34.72% 5615ms 6.15% std::_Rb_tree::_M_copy (inline) 5613ms 6.15% 40.87% 5613ms 6.15% boost::numeric::ublas::c_vector::operator() 11ms 0.012% 40.88% 5486ms 6.01% std::set::set (inline) 865ms 0.95% 41.83% 5452ms 5.97% AbstractMesh::GetDistanceBetweenNodes 4641ms 5.08% 46.91% 5331ms 5.84% _int_free 151ms 0.17% 47.08% 5129ms 5.62% SimpleWntCellCycleModel::GetWntLevel 557ms 0.61% 47.69% 4870ms 5.33% std::_Rb_tree::_M_clone_node (inline) 135ms 0.15% 47.84% 4861ms 5.32% WntConcentration::GetWntLevel 560ms 0.61% 48.45% 4746ms 5.20% boost::numeric::ublas::c_vector::operator[] (inline) 2143ms 2.35% 50.80% 4725ms 5.18% __cxxabiv1::__si_class_type_info::__do_dyncast 25ms 0.027% 50.83% 4683ms 5.13% MutableVertexMesh::RemoveDeletedNodes 3831ms 4.20% 55.02% 4625ms 5.07% _int_malloc 0 0% 55.02% 4622ms 5.06% std::insert_iterator::operator= (inline) 62ms 0.068% 55.09% 4544ms 4.98% EdgeHelper::RemoveDeletedEdges 1936ms 2.12% 57.21% 4444ms 4.87% std::_Rb_tree::_M_lower_bound (inline) 12ms 0.013% 57.22% 4308ms 4.72% EdgeHelper::UpdateEdgesMapKey 0 0% 57.22% 4279ms 4.69% std::_Rb_tree::_M_insert_unique_ (inline) 3957ms 4.33% 61.56% 3957ms 4.33% boost::numeric::ublas::same_impl_ex 0 0% 61.56% 3904ms 4.28% std::_Rb_tree::lower_bound (inline) 0 0% 61.56% 3904ms 4.28% std::map::lower_bound (inline) 30ms 0.033% 61.59% 3821ms 4.19% Cell::GetCellProliferativeType 0 0% 61.59% 3741ms 4.10% AbstractCellBasedSimulation::DoCellRemoval (inline) 91ms 0.1% 61.69% 3730ms 4.09% MutableElement::ResetIndex 59ms 0.065% 61.76% 3371ms 3.69% AbstractCellPopulation::GetCellUsingLocationIndex 151ms 0.17% 61.92% 3061ms 3.35% AbstractCellProperty::IsType (inline) 2932ms 3.21% 65.13% 2932ms 3.21% [libchaste_cell_based.so] 38ms 0.042% 65.17% 2888ms 3.16% SloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath 88ms 0.096% 65.27% 2863ms 3.14% Cell::SetCellProliferativeType 132ms 0.14% 65.41% 2699ms 2.96% boost::detail::shared_count::~shared_count (inline) 0 0% 65.41% 2699ms 2.96% boost::shared_ptr::~shared_ptr (inline) 0 0% 65.41% 2588ms 2.83% std::_Rb_tree::_M_insert_unique (inline) 215ms 0.24% 65.65% 2545ms 2.79% boost::numeric::ublas::vector_binary::size (inline) 2515ms 2.75% 68.41% 2526ms 2.77% boost::detail::sp_counted_base::release 616ms 0.67% 69.08% 2457ms 2.69% AbstractElement::GetNodeLocation 28ms 0.031% 69.11% 2453ms 2.69% std::_Rb_tree::_M_emplace_hint_unique 5ms 0.0055% 69.12% 2405ms 2.63% AbstractCellPopulation::Iterator::operator++ (inline) 169ms 0.19% 69.30% 2403ms 2.63% AbstractCellPopulation::Iterator::IsRealCell (inline) 0 0% 69.30% 2287ms 2.51% boost::numeric::ublas::c_vector::assign (inline) 0 0% 69.30% 2214ms 2.43% boost::numeric::ublas::c_vector::operator-= (inline) 0 0% 69.30% 2107ms 2.31% AbstractCellPopulation::WriteResultsToFiles 60ms 0.066% 69.37% 2102ms 2.30% std::_Rb_tree::erase 20ms 0.022% 69.39% 2084ms 2.28% Cell::GetCellData 2022ms 2.21% 71.60% 2022ms 2.21% [libchaste_mesh.so] 264ms 0.29% 71.89% 2016ms 2.21% std::_Rb_tree_const_iterator::operator++ (inline) 1998ms 2.19% 74.08% 1998ms 2.19% std::_Rb_tree::_S_right (inline) 45ms 0.049% 74.13% 1982ms 2.17% AbstractSimplePhaseBasedCellCycleModel::UpdateCellCyclePhase 247ms 0.27% 74.40% 1968ms 2.16% VertexMesh::GetAreaGradientOfElementAtNode 31ms 0.034% 74.44% 1945ms 2.13% CellPropertyCollection::HasProperty 0 0% 74.44% 1907ms 2.09% Cell::HasCellProperty (inline) 336ms 0.37% 74.80% 1870ms 2.05% AbstractCellProperty::IsSame 31ms 0.034% 74.84% 1861ms 2.04% VertexBasedCellPopulation::IsCellAssociatedWithADeletedLocation 0 0% 74.84% 1755ms 1.92% VertexBasedCellPopulation::WriteVtkResultsToFile 5ms 0.0055% 74.84% 1747ms 1.91% VertexBasedCellPopulation::WriteCellVtkResultsToFile 309ms 0.34% 75.18% 1686ms 1.85% VertexBasedCellPopulation::GetElementCorrespondingToCell (inline) 78ms 0.085% 75.27% 1640ms 1.80% VertexMesh::GetVolumeOfElement 0 0% 75.27% 1573ms 1.72% VertexMeshWriter::WriteVtkUsingMesh 136ms 0.15% 75.42% 1534ms 1.68% std::type_info::operator== (inline) 4ms 0.0044% 75.42% 1514ms 1.66% boost::numeric::ublas::vector_scalar_unary::evaluate (inline) 0 0% 75.42% 1514ms 1.66% boost::numeric::ublas::vector_scalar_unary::operator double (inline) 76ms 0.083% 75.50% 1507ms 1.65% MutableVertexMesh::CheckForSwapsFromShortEdges 0 0% 75.50% 1481ms 1.62% std::_Rb_tree::_Auto_node::_Auto_node (inline) 104ms 0.11% 75.62% 1425ms 1.56% CellPropertyCollection::AddProperty 0 0% 75.62% 1400ms 1.53% tcache_get (inline) 1400ms 1.53% 77.15% 1400ms 1.53% tcache_get_n (inline) 46ms 0.05% 77.20% 1393ms 1.53% AbstractCellPopulation::GetLocationIndexUsingCell 72ms 0.079% 77.28% 1354ms 1.48% VertexMesh::GetSurfaceAreaOfElement 1ms 0.0011% 77.28% 1320ms 1.45% OffLatticeSimulation::ApplyBoundaries 57ms 0.062% 77.34% 1285ms 1.41% std::_Rb_tree::_M_erase_aux (partial-inline) 1186ms 1.30% 78.64% 1186ms 1.30% std::_Rb_tree_increment 44ms 0.048% 78.69% 1158ms 1.27% CryptSimulationBoundaryCondition::VerifyBoundaryCondition 0 0% 78.69% 1131ms 1.24% boost::numeric::ublas::vector_binary::operator() (inline) 45ms 0.049% 78.74% 1072ms 1.17% CellPropertyRegistry::Get 14ms 0.015% 78.76% 1002ms 1.10% MutableElement::RegisterWithEdges (inline) 35ms 0.038% 78.79% 977ms 1.07% Edge::AddElement 78ms 0.085% 78.88% 976ms 1.07% boost::numeric::ublas::vector_reference::operator() (inline) 21ms 0.023% 78.90% 961ms 1.05% boost::numeric::ublas::detail::expression_type_check (inline) 34ms 0.037% 78.94% 942ms 1.03% Node::RemoveElement 0 0% 78.94% 939ms 1.03% CellPropertyCollection::~CellPropertyCollection (inline) 5ms 0.0055% 78.94% 911ms 1% std::set::erase (inline) 549ms 0.6% 79.55% 909ms 1% std::_Rb_tree::equal_range (inline) 145ms 0.16% 79.70% 904ms 0.99% boost::numeric::ublas::detail::equals 888ms 0.97% 80.68% 888ms 0.97% [libstdc++.so.6.0.33] 0 0% 80.68% 885ms 0.97% boost::numeric::ublas::norm_2 (inline) 639ms 0.7% 81.38% 884ms 0.97% CellPropertyCollection::GetProperty 869ms 0.95% 82.33% 869ms 0.95% std::_Rb_tree_insert_and_rebalance 451ms 0.49% 82.82% 854ms 0.94% boost::numeric::ublas::vector_norm_2::apply 8ms 0.0088% 82.83% 833ms 0.91% T2SwapCellKiller::CheckAndLabelCellsForApoptosisOrDeath 0 0% 82.83% 831ms 0.91% std::__new_allocator::destroy (inline) 0 0% 82.83% 831ms 0.91% std::allocator_traits::destroy (inline) 0 0% 82.83% 830ms 0.91% std::_Rb_tree::_M_destroy_node (inline) 0 0% 82.83% 819ms 0.9% boost::numeric::ublas::c_vector::assign_temporary (inline) 3ms 0.0033% 82.84% 819ms 0.9% boost::numeric::ublas::c_vector::swap (inline) 131ms 0.14% 82.98% 816ms 0.89% std::swap_ranges (inline) 0 0% 82.98% 795ms 0.87% VertexMeshWriter::MakeVtkMesh 0 0% 82.98% 790ms 0.87% std::_Rb_tree::clear (inline) 0 0% 82.98% 774ms 0.85% std::map::clear (inline) 773ms 0.85% 83.83% 773ms 0.85% tcache_put (inline) 745ms 0.82% 84.64% 745ms 0.82% Node::rGetLocation 336ms 0.37% 85.01% 722ms 0.79% std::_Rb_tree::_M_get_insert_hint_unique_pos (partial-inline) 61ms 0.067% 85.08% 703ms 0.77% boost::numeric::ublas::c_vector::operator= (inline) 46ms 0.05% 85.13% 686ms 0.75% std::less::operator() (inline) 0 0% 85.13% 685ms 0.75% std::iter_swap (inline) 685ms 0.75% 85.88% 685ms 0.75% std::swap (inline) 87ms 0.095% 85.97% 647ms 0.71% MutableElement::GetNodeLocalIndex 0 0% 85.97% 640ms 0.7% boost::numeric::ublas::norm_inf (inline) 244ms 0.27% 86.24% 640ms 0.7% boost::numeric::ublas::vector_norm_inf::apply (inline) 491ms 0.54% 86.78% 640ms 0.7% std::operator< (inline) 85ms 0.093% 86.87% 631ms 0.69% std::_Rb_tree::find (inline) 0 0% 86.87% 607ms 0.66% std::_Rb_tree::_Auto_node::_M_insert (inline) 22ms 0.024% 86.89% 607ms 0.66% std::_Rb_tree::_M_insert_node (inline) 604ms 0.66% 87.56% 604ms 0.66% std::vector::size (inline) 0 0% 87.56% 568ms 0.62% vtkPolygon::New 0 0% 87.56% 567ms 0.62% vtkPolygon::vtkPolygon 2ms 0.0022% 87.56% 533ms 0.58% std::map::find (inline) 528ms 0.58% 88.14% 528ms 0.58% Node::GetIndex 5ms 0.0055% 88.14% 516ms 0.57% boost::numeric::ublas::unbounded_array::unbounded_array (inline) 0 0% 88.14% 516ms 0.57% boost::numeric::ublas::vector::vector (inline) 0 0% 88.14% 511ms 0.56% std::_Vector_base::_M_allocate (inline) 0 0% 88.14% 498ms 0.55% std::map::map (inline) 17ms 0.019% 88.16% 473ms 0.52% MutableElement::RegisterWithNodes (inline)